If the publisher has requested duotones your best bet will be to produce or manipulate your images, using a program like Adobe's photoshop or just provide good resolutions of the original raw images to the publisher or color lab.
For scientific images you maybe able to produce the duotones using imageJ. Besides being open source is an excellent package and worth having it for other purposes also.
It is not possible with current PDF technology to automatically modify an included image and change it to a duotone, even with Acrobat Professional. You will need the full stack and knowledge of Adobe's workflow tools to do so. To see the difficulties try this minimal with an appropriate image, which converts an image to a two channel colour.
\documentclass[a4paper]{article}
\usepackage{graphicx}
\begin{document}
\includegraphics[width=5cm]{blue.jpg}% image with RGB colors
\includegraphics[decodearray= 0.5 1.0
0.0 0.0
0.0 0.0, width=5cm]{blue.jpg}%
\end{document}
This changes the color of the image (original at left) to an almost sepia color (image from wikipedia link above).

An additional consideration is that the final printed image, irrespective of the image format used, can very considerably from what your eye perceives on a screen. The sad truth is that no printing technology can reproduce the bright, saturated colors your monitor displays. Equally true that print can reproduce colors that a monitor cannot display, such as metallics and fluorescents and more importantly, dark saturated colors, particularly the yellows, oranges, greens and cyans.
Best advice I can offer is to suggest you talk to the publisher and get advice, as to what is the minimum that they would require and in what format.
(normally they would require .tiff images).